title: Replication of nonautonomous retroelements in soybean appears to be both recent and common.
abstract: Retrotransposons and their remnants often constitute more than 50% of higher plant genomes. Although extensively studied in monocot crops such as maize (Zea mays) and rice (Oryza sativa), the impact of retrotransposons on dicot crop genomes is not well documented. Here, we present an analysis of retrotransposons in soybean (Glycine max). Analysis of approximately 3.7 megabases (Mb) of genomic sequence, including 0.87 Mb of pericentromeric sequence, uncovered 45 intact long terminal repeat (LTR)-retrotransposons. The ratio of intact elements to solo LTRs was 8:1, one of the highest reported to date in plants, suggesting that removal of retrotransposons by homologous recombination between LTRs is occurring more slowly in soybean than in previously characterized plant species. Analysis of paired LTR sequences uncovered a low frequency of deletions relative to base substitutions, indicating that removal of retrotransposon sequences by illegitimate recombination is also operating more slowly. Significantly, we identified three subfamilies of nonautonomous elements that have replicated in the recent past, suggesting that retrotransposition can be catalyzed in trans by autonomous elements elsewhere in the genome. Analysis of 1.6 Mb of sequence from Glycine tomentella, a wild perennial relative of soybean, uncovered 23 intact retroelements, two of which had accumulated no mutations in their LTRs, indicating very recent insertion. A similar pattern was found in 0.94 Mb of sequence from Phaseolus vulgaris (common bean). Thus, autonomous and nonautonomous retrotransposons appear to be both abundant and active in Glycine and Phaseolus. The impact of nonautonomous retrotransposon replication on genome size appears to be much greater than previously appreciated.
authors.affiliation: Department of Biology, Indiana University, Bloomington, Indiana 47405, USA.
authors.forename: Adam
authors.initials: A
authors.lastname: Wawrzynski
authors.forename: Tom
authors.initials: T
authors.lastname: Ashfield
authors.forename: Nicolas W G
authors.initials: NW
authors.lastname: Chen
authors.forename: Jafar
authors.initials: J
authors.lastname: Mammadov
authors.forename: Ashley
authors.initials: A
authors.lastname: Nguyen
authors.forename: Ram
authors.initials: R
authors.lastname: Podicheti
authors.forename: Steven B
authors.initials: SB
authors.lastname: Cannon
authors.forename: Vincent
authors.initials: V
authors.lastname: Thareau
authors.forename: Carine
authors.initials: C
authors.lastname: Ameline-Torregrosa
authors.forename: Ethalinda
authors.initials: E
authors.lastname: Cannon
authors.forename: Ben
authors.initials: B
authors.lastname: Chacko
authors.forename: Arnaud
authors.initials: A
authors.lastname: Couloux
authors.forename: Anita
authors.initials: A
authors.lastname: Dalwani
authors.forename: Roxanne
authors.initials: R
authors.lastname: Denny
authors.forename: Shweta
authors.initials: S
authors.lastname: Deshpande
authors.forename: Ashley N
authors.initials: AN
authors.lastname: Egan
authors.forename: Natasha
authors.initials: N
authors.lastname: Glover
authors.forename: Stacy
authors.initials: S
authors.lastname: Howell
authors.forename: Dan
authors.initials: D
authors.lastname: Ilut
authors.forename: Hongshing
authors.initials: H
authors.lastname: Lai
authors.forename: Sara Martin
authors.initials: SM
authors.lastname: Del Campo
authors.forename: Michelle
authors.initials: M
authors.lastname: Metcalf
authors.forename: Majesta
authors.initials: M
authors.lastname: O'Bleness
authors.forename: Bernard E
authors.initials: BE
authors.lastname: Pfeil
authors.forename: Milind B
authors.initials: MB
authors.lastname: Ratnaparkhe
authors.forename: Sylvie
authors.initials: S
authors.lastname: Samain
authors.forename: Iryna
authors.initials: I
authors.lastname: Sanders
authors.forename: Béatrice
authors.initials: B
authors.lastname: Ségurens
authors.forename: Mireille
authors.initials: M
authors.lastname: Sévignac
authors.forename: Sue
authors.initials: S
authors.lastname: Sherman-Broyles
authors.forename: Dominic M
authors.initials: DM
authors.lastname: Tucker
authors.forename: Jing
authors.initials: J
authors.lastname: Yi
authors.forename: Jeff J
authors.initials: JJ
authors.lastname: Doyle
authors.forename: Valérie
authors.initials: V
authors.lastname: Geffroy
authors.forename: Bruce A
authors.initials: BA
authors.lastname: Roe
authors.forename: M A Saghai
authors.initials: MA
authors.lastname: Maroof
authors.forename: Nevin D
authors.initials: ND
authors.lastname: Young
authors.forename: Roger W
authors.initials: RW
authors.lastname: Innes
mesh_terms: D001483:Base Sequence; D018744:DNA, Plant / Q000737:chemistry; D019143:Evolution, Molecular; D017353:Gene Deletion; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D020084:Long Interspersed Nucleotide Elements; D008745:Methylation; D016254:Mutagenesis, Insertional; D027805:Phaseolus / Q000235:genetics; D010802:Phylogeny; D018626:Retroelements; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D013025:Glycine max / Q000235:genetics*; D020079:Terminal Repeat Sequences
chemical_list: D018744:DNA, Plant; D018626:Retroelements